Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost

Characterization and analysis of a Commiphora species germinated from an ancient seed suggests a possible connection to a species mentioned in the Bible

A seed recovered during archaeological excavations of a cave in the Judean desert was germinated, with radiocarbon analysis indicating an age of 993 CE- 1202 calCE. DNA sequencing and phylogenetic analysis identified the seedling as belonging to the angiosperm genus Commiphora Jacq., sister to three Southern African Commiphora species, but unique from all other species sampled to date. The germinated seedling was not closely related to Commiphora species commonly harvested for their fragrant oleoresins including Commiphora gileadensis (L.) C.Chr., candidate for the locally extinct "Judean Balsam" or "Balm of Gilead" of antiquity. GC-MS analysis revealed minimal fragrant compounds but abundance of those associated with multi-target bioactivity and a previously undescribed glycolipid compound series. Several hypotheses are offered to explain the origins, implications and ethnobotanical significance of this unknown Commiphora sp., to the best of our knowledge the first identified from an archaeological site in this region, including identification with a resin producing tree mentioned in Biblical sources and possible agricultural relationship with the historic Judean Balsam.

Programmed ageing: decline of stem cell renewal, immunosenescence, and Alzheimer's disease

The characteristic maximum lifespan varies enormously across animal species from a few hours to hundreds of years. This argues that maximum lifespan, and the ageing process that itself dictates lifespan, are to a large extent genetically determined. Although controversial, this is supported by firm evidence that semelparous species display evolutionarily programmed ageing in response to reproductive and environmental cues. Parabiosis experiments reveal that ageing is orchestrated systemically through the circulation, accompanied by programmed changes in hormone levels across a lifetime. This implies that, like the circadian and circannual clocks, there is a master 'clock of age' (circavital clock) located in the limbic brain of mammals that modulates systemic changes in growth factor and hormone secretion over the lifespan, as well as systemic alterations in gene expression as revealed by genomic methylation analysis. Studies on accelerated ageing in mice, as well as human longevity genes, converge on evolutionarily conserved fibroblast growth factors (FGFs) and their receptors, including KLOTHO, as well as insulin-like growth factors (IGFs) and steroid hormones, as key players mediating the systemic effects of ageing. Age-related changes in these and multiple other factors are inferred to cause a progressive decline in tissue maintenance through failure of stem cell replenishment. This most severely affects the immune system, which requires constant renewal from bone marrow stem cells. Age-related immune decline increases risk of infection whereas lifespan can be extended in germfree animals. This and other evidence suggests that infection is the major cause of death in higher organisms. Immune decline is also associated with age-related diseases. Taking the example of Alzheimer's disease (AD), we assess the evidence that AD is caused by immunosenescence and infection. The signature protein of AD brain, Aβ, is now known to be an antimicrobial peptide, and Aβ deposits in AD brain may be a response to infection rather than a cause of disease. Because some cognitively normal elderly individuals show extensive neuropathology, we argue that the location of the pathology is crucial - specifically, lesions to limbic brain are likely to accentuate immunosenescence, and could thus underlie a vicious cycle of accelerated immune decline and microbial proliferation that culminates in AD. This general model may extend to other age-related diseases, and we propose a general paradigm of organismal senescence in which declining stem cell proliferation leads to programmed immunosenescence and mortality.

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus kolymaensis. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in P. kolymaensis and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

Choosing the Right Path for the Successful Storage of Seeds

Seeds are the most commonly used source of storage material to preserve the genetic diversity of plants. However, prior to the deposition of seeds in gene banks, several questions need to be addressed. Here, we illustrate the scheme that can be used to ensure that the most optimal conditions are identified to enable the long-term storage of seeds. The main questions that need to be answered pertain to the production of viable seeds by plants, the availability of proper protocols for dormancy alleviation and germination, seed tolerance to desiccation and cold storage at -20 °C. Finally, it is very important to fully understand the capability or lack thereof for seeds or their explants to tolerate cryogenic conditions. The proper storage regimes for orthodox, intermediate and recalcitrant seeds are discussed.

Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity

Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.

Past and present giant viruses diversity explored through permafrost metagenomics

Giant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families.

Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources

Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.

Approaches for the complex assessment of polychemical pollution of permafrost-affected soils and the upper layer of permafrost

The analysis of about 200 samples taken from 42 permafrost-affected soil profiles was carried out on four key sites in different regions of cryolithozone (West Siberia, Central, North, and North-East Yakutia) characterized by different active layer depths and soil lithology. The aim of the study was to determine the influence of different processes of cryogenic mass-exchange on the redistribution and accumulation of major pollutants such as petroleum products, acid-soluble forms of trace elements, polycyclic hydrocarbons, and technogenic radionuclides transferred via atmospheric transport or after the local anthropogenic impact in different soil horizons of Cryosols and in the upper layers of permafrost. Samples were analyzed using modern precise techniques (direct γ-spectrometric measurements with Ge(Li) and NaI(Tl) detectors; fluorometric method; reversed-phase high-performance liquid chromatography; spectrofluorimetric detection; atomic absorption spectrometry with flame atomization). The study has shown that processes (cryoturbations, frost heaving, gelifluction along with fluvial processes) that strongly affect Cryosols' profile structure can also lead to the active migration and accumulation of local and global pollutants in the middle and lowermost suprapermafrost soil horizons. The accumulation of some pollutants in suprapermafrost horizons of cryogenic soils and in the upper layers of permafrost (in particular, petroleum products and mobile forms of trace elements) can be associated with a combination of factors, such as the relatively light particle size distribution, relatively weak manifestation of cryoturbation processes, and low thickness of the active layer (about 40-60 cm). The integral calculation of the geoaccumulation index values has shown that all of the groups of human-affected soil horizons are moderately to extremely polluted by petroleum hydrocarbons (and at a relatively lower level by trace elements) and the maximum pollution stands for the suprapermafrost horizons as well as in cryoturbated or buried fragments of organogenic matter in some cases. The maxima of the heavy PAH content in permafrost-affected soils can be confined to horizons enriched with anthropogenic inclusions and artifacts (for example, construction slag, coal) and to individual horizons of soils buried as a result of both cryogenic and alluvial processes. The specific activity of the technogenic radionuclide cesium in cryogenic soils revealed its association mainly with the surface organogenic and organomineral horizons of the studied profiles and rarely observed in the cryoturbated fragments of these horizons in the middle and suprapermafrost layers of soil profiles. The necessity of the complex analytical assessment of the permafrost-affected soils has been revealed especially in case of studying of the ecological state of the anthropogenically affected Cryosols.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

Evaluating the Microbial Habitability of Rogue Planets and Proposing Speculative Scenarios on How They Might Act as Vectors for Panspermia

There are two types of rogue planets, sub-brown dwarfs and “rocky” rogue planets. Sub-brown dwarfs are unlikely to be habitable or even host life, but rocky rogue planets may have a liquid ocean under a thick atmosphere or an ice layer. If they are overlain by an insulating ice layer, they are also referred to as Steppenwolf planets. However, given the poor detectability of rocky rogue planets, there is still no direct evidence of the presence of water or ice on them. Here we discuss the possibility that these types of rogue planets could harbor unicellular organisms, conceivably based on a variety of different energy sources, including chemical, osmotic, thermal, and luminous energy. Further, given the theoretically predicted high number of rogue planets in the galaxy, we speculate that rogue planets could serve as a source for galactic panspermia, transferring life to other planetary systems.

A living bdelloid rotifer from 24,000-year-old Arctic permafrost

In natural, permanently frozen habitats, some organisms may be preserved for hundreds to tens of thousands of years. For example, stems of Antarctic moss were successfully regrown from an over millennium-old sample covered by ice for about 400 years¹. Likewise, whole campion plants were regenerated from seed tissue preserved in relict 32,000-year-old permafrost², and nematodes were revived from the permafrost of two localities in northeastern Siberia, with source sediments dated over 30,000 years BP³. Bdelloid rotifers, microscopic multicellular animals, are known for their ability to survive extremely low temperatures⁴. Previous reports suggest survival after six to ten years when frozen between -20° to 0°C^4-6. Here, we report the survival of an obligate parthenogenetic bdelloid rotifer, recovered from northeastern Siberian permafrost radiocarbon-dated to ∼24,000 years BP. This constitutes the longest reported case of rotifer survival in a frozen state. We confirmed the finding by identifying rotifer actin gene sequences in a metagenome obtained from the same sample. By morphological and molecular markers, the discovered rotifer belongs to the genus Adineta, and aligns with a contemporary Adineta vaga isolate collected in Belgium. Experiments demonstrated that the ancient rotifer withstands slow cooling and freezing (∼1°C min^-1) for at least seven days. We also show that a clonal culture can continuously reproduce in the laboratory by parthenogenesis.

The genomes of ancient date palms germinated from 2,000 y old seeds

Resurrection genomics is an alternative to ancient DNA approaches in studying the genetics and evolution of past and possibly extinct populations. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, one can study genomes of lost populations. We applied this approach by sequencing the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from ∼2,000 y old seeds recovered in the Southern Levant. Using this genomic data, we were able to document that introgressive hybridization of the wild Cretan palm Phoenix theophrasti into date palms had occurred in the Eastern Mediterranean by ∼2,200 y ago and examine the evolution of date palm populations in this pivotal region two millennia ago.

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth?

The present world faces a new threat of ancient microbes and resistomes that are locked in the cryosphere and now releasing upon thawing due to climate change and anthropogenic activities. The cryosphere act as the best preserving place for these microbes and resistomes that stay alive for millions of years. Current reviews extensively discussed whether the resurrection of microbes and resistomes existing in these pristine environments is true or just a hype. Release of these ancient microorganisms and naked DNA is of great concern for society as these microbes can either cause infections directly or they can interact with contemporary microorganisms and affect their fitness, survival, and mutation rate. Moreover, the contemporary microorganisms may uptake the unlocked naked DNA, which might transform non-pathogenic microorganisms into deadly antibiotic-resistant microbes. Additionally, the resurrection of glacial microorganisms can cause adverse effects on ecosystems downstream. The release of glacial pathogens and naked DNA is real and can lead to fatal outbreaks; therefore, we must prepare ourselves for the possible reemergence of diseases caused by these microbes. This study provides a scientific base for the adoption of actions by international cooperation to develop preventive measures.

Trade-off between seed dispersal in space and time

Seed movement and delayed germination have long been thought to represent alternative risk-spreading strategies, but current evidence covers limited scales and yields mixed results. Here we present the first global-scale test of a negative correlation between dispersal and dormancy. The result demonstrates a strong and consistent pattern that species with dormant seeds have reduced spatial dispersal, also in the context of life-history traits such as seed mass and plant lifespan. Long-lived species are more likely to have large, non-dormant seeds that are dispersed far. Our findings provide robust support for the theoretical prediction of a dispersal trade-off between space and time, implying that a joint consideration of risk-spreading strategies is imperative in studying plant life-history evolution. The bet-hedging patterns in the dispersal-dormancy correlation and the associated reproductive traits have implications for biodiversity conservation, via prediction of which plant groups would be most impacted in the changing era.

Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses

Background

Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to 1000 metres depth. Due to constant subzero temperatures, permafrost represents a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several protist strains and two giant protist viruses isolated from permafrost cores have been already described.

New information

In this paper, we describe a collection of 35 amoeboid protist strains isolated from the samples of Holocene and Pleistocene permanently frozen sediments. These samples are stored at −18°C in the Soil Cryology Lab, Pushchino, Russia and may be used for further studies and isolation attempts. The collection strains are maintained in liquid media and may be available upon request. The paper also presents a dataset which consists of a table describing the samples and their properties (termed "Sampling events") and a table describing the isolated strains (termed "Occurrences"). The dataset is publicly available through the GBIF portal.

Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life

Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.

Ex situ collections and their potential for the restoration of extinct plants

The alarming current and predicted species extinction rates have galvanized conservationists in their efforts to avoid future biodiversity losses, but for species extinct in the wild, few options exist. We posed the questions, can these species be restored, and, if so, what role can ex situ plant collections (i.e., botanic gardens, germplasm banks, herbaria) play in the recovery of plant genetic diversity? We reviewed the relevant literature to assess the feasibility of recovering lost plant genetic diversity with using ex situ material and the probability of survival of subsequent translocations. Thirteen attempts to recover species extinct in the wild were found, most of which used material preserved in botanic gardens (12) and seed banks (2). One case of a locally extirpated population was recovered from herbarium material. Eight (60%) of these cases were successful or partially successful translocations of the focal species or population; the other 5 failed or it was too early to determine the outcome. Limiting factors of the use of ex situ source material for the restoration of plant genetic diversity in the wild include the scarcity of source material, low viability and reduced longevity of the material, low genetic variation, lack of evolution (especially for material stored in germplasm banks and herbaria), and socioeconomic factors. However, modern collecting practices present opportunities for plant conservation, such as improved collecting protocols and improved cultivation and storage conditions. Our findings suggest that all types of ex situ collections may contribute effectively to plant species conservation if their use is informed by a thorough understanding of the aforementioned problems. We conclude that the recovery of plant species currently classified as extinct in the wild is not 100% successful, and the possibility of successful reintroduction should not be used to justify insufficient in situ conservation.

Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses

Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry.IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.

Age-dependent loss of seed viability is associated with increased lipid oxidation and hydrolysis

The accumulation of reactive oxygen species has been associated with a loss of seed viability. Therefore, we have investigated the germination ability of a range of seed stocks, including two wheat collections and one barley collection that had been dry-aged for 5-40 years. Metabolite profiling analysis revealed that the accumulation of glycerol was negatively correlated with the ability to germinate in all seed sets. Furthermore, lipid degradation products such as glycerol phosphates and galactose were accumulated in some seed sets. A quantitative analysis of nonoxidized and oxidized lipids was performed in the wheat seed set that showed the greatest variation in germination. This analysis revealed that the levels of fully acylated and nonoxidized storage lipids like triacylglycerols and structural lipids like phospho- and galactolipids were decreasing. Moreover, the abundance of oxidized variants and hydrolysed products such as mono-/diacylglycerols, lysophospholipids, and fatty acids accumulated as viability decreased. The proportional formation of oxidized and nonoxidized fatty acids provides evidence for an enzymatic hydrolysis of specifically oxidized lipids in dry seeds. The results link reactive oxygen species with lipid oxidation, structural damage, and death in long-term aged seeds.

How contraction has shaped evolution

Two unicellular relatives of animals reveal that coordinated contractions of groups of cells using actomyosin predated animal multicellularity during evolution.

Microsite conditions in retrogressive thaw slumps may facilitate increased seedling recruitment in the Alaskan Low Arctic

In Low Arctic tundra, thermal erosion of ice-rich permafrost soils (thermokarst) has increased in frequency since the 1980s. Retrogressive thaw slumps (RTS) are thermokarst disturbances forming large open depressions on hillslopes through soil wasting and vegetation displacement. Tall (>0.5 m) deciduous shrubs have been observed in RTS a decade after disturbance. RTS may provide conditions suitable for seedling recruitment, which may contribute to Arctic shrub expansion. We quantified in situ seedling abundance, and size and viability of soil seedbanks in greenhouse trials for two RTS chronosequences near lakes on Alaska's North Slope. We hypothesized recent RTS provide microsites for greater recruitment than mature RTS or undisturbed tundra. We also hypothesized soil seedbanks demonstrate quantity-quality trade-offs; younger seedbanks contain smaller numbers of mostly viable seed that decrease in viability as seed accumulates over time. We found five times as many seedlings in younger RTS as in older RTS, including birch and willow, and no seedlings in undisturbed tundra. Higher seedling counts were associated with bare soil, warmer soils, higher soil available nitrogen, and less plant cover. Seedbank viability was unrelated to size. Older seedbanks were larger at one chronosequence, with no difference in percent germination. At the other chronosequence, germination was lower from older seedbanks but seedbank size was not different. Seedbank germination was positively associated with in situ seedling abundance at one RTS chronosequence, suggesting postdisturbance revegetation from seedbanks. Thermal erosion may be important for recruitment in tundra by providing bare microsites that are warmer, more nutrient-rich, and less vegetated than in undisturbed ground. Differences between two chronosequences in seedbank size, viability, and species composition suggest disturbance interacts with local conditions to form seedbanks. RTS may act as seedling nurseries to benefit many Arctic species as climate changes, particularly those that do not produce persistent seed.

The Ancestral Process of Long-Range Seed Bank Models

We present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright‒Fisher model, as well as a seed bank model with bounded age distribution considered in Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that, for age distributions with finite mean, the ancestral process converges to a time-changed Kingman coalescent, while in the case of infinite mean, ancestral lineages might not merge at all with positive probability. Furthermore, we present a construction of the forward-in-time process in equilibrium. The mathematical methods are based on renewal theory, the urn process introduced in Kaj, Krone and Lascoux (2001) as well as on a paper by Hammond and Sheffield (2013).

Resurrection of Dormant Daphnia magna: Protocol and Applications

Long-term studies enable the identification of eco-evolutionary processes that occur over extended time periods. In addition, they provide key empirical data that may be used in predictive modelling to forecast evolutionary responses of natural ecosystems to future environmental changes. However, excluding a few exceptional cases, long-term studies are scarce because of logistic difficulties associated with accessing temporal samples. Temporal dynamics are frequently studied in the laboratory or in controlled mesocosm experiments with exceptional studies that reconstruct the evolution of natural populations in the wild.

Here, a standard operating procedure (SOP) is provided to revive or resurrect dormant Daphnia magna, a widespread zooplankton keystone species in aquatic ecosystems, to dramatically advance the state-of-the-art longitudinal data collection in natural systems. The field of Resurrection Ecology was defined in 1999 by Kerfoot and co-workers, even though the first attempts at hatching diapausing zooplankton eggs date back to the late 1980s. Since Kerfoot's seminal paper, the methodology of resurrecting zooplankton species has been increasingly frequently applied, though propagated among laboratories only via direct knowledge transfer. Here, an SOP is described that provides a step-by-step protocol on the practice of resurrecting dormant Daphnia magna eggs.

Two key studies are provided in which the fitness response of resurrected Daphnia magna populations to warming is measured, capitalizing on the ability to study historical and modern populations in the same settings. Finally, the application of next generation sequencing technologies to revived or still dormant stages is discussed. These technologies provide unprecedented power in dissecting the processes and mechanisms of evolution if applied to populations that have experienced changes in selection pressure over time.

Evolutionary aspects of resurrection ecology: Progress, scope, and applications-An overview

This perspective provides an overview to the Special Issue on Resurrection Ecology (RE). It summarizes the contributions to this Special Issue, and provides background information and future prospects for the use of RE in both basic and applied evolutionary studies.

The paleosymbiosis hypothesis: host plants can be colonised by root symbionts that have been inactive for centuries to millenia

Paleoecologists have speculated that post-glacial migration of tree species could have been facilitated by mycorrhizal symbionts surviving glaciation as resistant propagules belowground. The general premise of this idea, which we call the 'paleosymbiosis hypothesis', is that host plants can access and be colonised by fungal root symbionts that have been inactive for millennia. Here, we explore the plausibility of this hypothesis by synthesising relevant findings from a diverse literature. For example, the paleoecology literature provided evidence of modern roots penetrating paleosols containing ancient (>6000 years) fungal propagules, though these were of unknown condition. With respect to propagule longevity, the available evidence is of mixed quality, but includes convincing examples consistent with the paleosymbiosis hypothesis (i.e. >1000 years viable propagules). We describe symbiont traits and environmental conditions that should favour the development and preservation of an ancient propagule bank, and discuss the implications for our understanding of soil symbiont diversity and ecosystem functioning. We conclude that the paleosymbiosis hypothesis is plausible in locations where propagule deposition and preservation conditions are favourable (e.g. permafrost regions). We encourage future belowground research to consider and explore the potential temporal origins of root symbioses.

Re-emerging infectious diseases from the past: Hysteria or real risk?

BACKGROUND

Work on human remains and old biological samples is a potential source of contamination by conventional or atypical infectious agents. Similarly, current and future environmental changes are a source of resurgence of ancient epidemic diseases. To what extent are anthropologists sorcerer apprentices (especially those working on ancient samples, i.e. paleo-anthropologists)? Are ancient skeletons, palaeosols and museum objects with a biological component at risk for current populations? Unless there are unfounded fears and undue risk… What can be learned from the recent scientific literature and the common sense of the researchers?

METHODS

We have attempted to compile data from the literature and from our personal experience in the fields of anthropology, clinical medicine and epidemiology, in order to grasp the reality of the risk to the human population.

RESULTS

It appears that the risk is real, but extremely limited. Specific and simple protective measures must be taken in terms of overall and individual health, both in the field and in the laboratory.

CONCLUSION

These data are important for the internist, due to the possibility of atypical infections, both in specialized workers and in populations at risk (environmental context).

Moss survival through in situ cryptobiosis after six centuries of glacier burial

Cryptobiosis is a reversible ametabolic state of life characterized by the ceasing of all metabolic processes, allowing survival of periods of intense adverse conditions. Here we show that 1) entire moss individuals, dated by 14C, survived through cryptobiosis during six centuries of cold-based glacier burial in Antarctica, 2) after re-exposure due to glacier retreat, instead of dying (due to high rates of respiration supporting repair processes), at least some of these mosses were able to return to a metabolically active state and remain alive. Moss survival was assessed through growth experiments and, for the first time, through vitality measurements. Future investigations on the genetic pathways involved in cryptobiosis and the subsequent recovery mechanisms will provide key information on their applicability to other systematic groups, with implications for fields as divergent as medicine, biodiversity conservation, agriculture and space exploration.

Physical mechanism for biopolymers to aggregate and maintain in non-equilibrium states

Many human or animal diseases are related to aggregation of proteins. A viable biological organism should maintain in non-equilibrium states. How protein aggregate and why biological organisms can maintain in non-equilibrium states are not well understood. As a first step to understand such complex systems problems, we consider simple model systems containing polymer chains and solvent particles. The strength of the spring to connect two neighboring monomers in a polymer chain is controlled by a parameter s with s → ∞ for rigid-bond. The strengths of bending and torsion angle dependent interactions are controlled by a parameter s A with s A  → -∞ corresponding to no bending and torsion angle dependent interactions. We find that for very small s A , polymer chains tend to aggregate spontaneously and the trend is independent of the strength of spring. For strong springs, the speed distribution of monomers in the parallel (along the direction of the spring to connect two neighboring monomers) and perpendicular directions have different effective temperatures and such systems are in non-equilibrium states.

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.

Experimental macroevolution

The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.

Dry seeds and environmental extremes: consequences for seed lifespan and germination

In the context of climate change, food security and long-term human space missions, it is important to understand which species produce seeds that can tolerate extreme environmental conditions. Here we consider dry seed survival of extreme conditions encountered in both natural and artificially controlled environments. Considerable overlap exists between the two: for example, ultra-dry and anoxic conditions can be artificially imposed during seed storage and also occur naturally in the vacuum of space environments. Aside from ultra-drying and anoxia, dry seeds of many species may experience extremely high temperatures due to heat from wildfires or when exposed to solar heat in biomes such as deserts. In addition, seeds can be irradiated by UV-A and UV-B at the surface of the Earth and by the shorter wavelengths of UV-C in outer space. We focus on the effects of these extreme environmental conditions on dry seed lifespan and germination. Although it is clear that seeds from particular plant species and families can tolerate exposures to ultra-drying, high temperatures (at least 32 families) or UV radiation with minimal consequences for subsequent germination ability, further research is needed to elucidate many of the mechanisms underlying extreme tolerance of these environmental conditions found on Earth or in space.

The Ancestral Process of Long-Range Seed Bank Models

We present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright‒Fisher model, as well as a seed bank model with bounded age distribution considered in Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that, for age distributions with finite mean, the ancestral process converges to a time-changed Kingman coalescent, while in the case of infinite mean, ancestral lineages might not merge at all with positive probability. Furthermore, we present a construction of the forward-in-time process in equilibrium. The mathematical methods are based on renewal theory, the urn process introduced in Kaj, Krone and Lascoux (2001) as well as on a paper by Hammond and Sheffield (2013).

Production of viable trout offspring derived from frozen whole fish

Long-term preservation of fish fertility is essential for the conservation of endangered fishes. However, cryopreservation techniques for fish oocytes and embryos have not yet been developed. In the present study, functional eggs and sperm were derived from whole rainbow trout that had been frozen in a freezer and stored without the aid of exogenous cryoprotectants. Type A spermatogonia retrieved from frozen-thawed whole trout remained viable after freezing duration up to 1,113 days. Long-term-frozen trout spermatogonia that were intraperitoneally transplanted into triploid salmon hatchlings migrated toward the recipient gonads, where they were incorporated, and proliferated rapidly. Although all triploid recipients that did not undergo transplantation were functionally sterile, 2 of 12 female recipients and 4 of 13 male recipients reached sexual maturity. Eggs and sperm obtained from the salmon recipients were capable of producing donor-derived trout offspring. This methodology is thus a convenient emergency tool for the preservation of endangered fishes.

Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog

Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.

Aging and longevity in the simplest animals and the quest for immortality

Here we review the examples of great longevity and potential immortality in the earliest animal types and contrast and compare these to humans and other higher animals. We start by discussing aging in single-celled organisms such as yeast and ciliates, and the idea of the immortal cell clone. Then we describe how these cell clones could become organized into colonies of different cell types that lead to multicellular animal life. We survey aging and longevity in all of the basal metazoan groups including ctenophores (comb jellies), sponges, placozoans, cnidarians (hydras, jellyfish, corals and sea anemones) and myxozoans. Then we move to the simplest bilaterian animals (with a head, three body cell layers, and bilateral symmetry), the two phyla of flatworms. A key determinant of longevity and immortality in most of these simple animals is the large numbers of pluripotent stem cells that underlie the remarkable abilities of these animals to regenerate and rejuvenate themselves. Finally, we discuss briefly the evolution of the higher bilaterians and how longevity was reduced and immortality lost due to attainment of greater body complexity and cell cycle strategies that protect these complex organisms from developing tumors. We also briefly consider how the evolution of multiple aging-related mechanisms/pathways hinders our ability to understand and modify the aging process in higher organisms.

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.